I only know 3DS Max, But I could probably give you a general sense of what's happening.
When I import SWG models, it gets split into separate meshes, depending on what parts of the mesh the Shader/Texture is applied to. Each of these parts have their own, separate UV maps.
If I want to I can then recombine them into one solid mesh, and apply the different materials, to individual faces on separate material "channels". And then it would likely be the same scenario you have there. (maybe in your case you need to separate them into different meshes, so it's easier to work with.)
Example - The animated screen on the Bank Terminal is a separate, Material/texture from the rest of the bank terminal; as well as the "instrument panel" material.
As for how this gets translated back to SWG, I have no idea. It would depend on the Export plugin/script, which I haven't spent much time with.